Recognition of oligiosaccaride molecular targets by polycationic small molecule inhibitors and treatment of immunological disorders and infectious diseases

ABSTRACT

Small molecule polycationic agents are used to modulate or interrupt biological processes by binding to oligosaccharide-based biomolecules. Compounds that inhibit nitric oxide, TNFα or other immunomodulators are provided and are useful for treating immunological disease and disease of an infectious disorder.

TECHNICAL FIELD

The present disclosure relates to certain polycationic compounds. Thepresent disclosure also relates to methods and compositions that can beused to define drug targets, setup screening assays and the design ofagents to interrupt pathological biological processes involvingcarbohydrate targets. The present disclosure also relates to drug agentsused to treat diseases or conditions, particularly immunologicaldisorders and infectious diseases.

Small molecule polycationic compounds bind and neutralize bacteriallipopolysaccharides, and along with test results suggest theirsuitability for the prevention or treatment of endotoxic shock states orsepsis.

BACKGROUND

Carbohydrates represent the bulk of organic matter on earth.¹ It hasbeen noted that roughly 80% of secreted and cell-surface proteins areglycosylated.² The scientific field of glycobiology involves theinvestigation of the role that saccharide structure plays in biologicalfunction. Given the generally complex structural nature ofglycoconjugates, this has been the last of the three major biologicalmaterials to be explored in great detail. Unlike proteins and nucleicacids, the biosynthesis of glycosylated biostructures does not involve atemplated, message-driven production. A diverse set of enzymes operateon substrates to synthesize three main types of glycoconjugates: 1)N-linked glycoproteins, 2) O-linked glycoproteins and 3)glycosaminoglycans.³

The role of oligosaccharides in biological recognition has been amplydemonstrated in recent scientific literature. This role extends to celladhesion, cell-to-cell communications and signal transduction, route toinfection by bacteria and viruses, development and immunology.⁴ It hasbeen noted that almost all of the key molecules involved in the innateand adaptive immune response are glycoproteins.⁵

The specific biological recognition of saccharides is a tremendouschemical challenge, even for nature, due to their complex, irregular andmultifunctional structures.⁶ This challenge is made even more difficultby the ability of the poly-hydroxylated exteriors to associate well withwater. It has been noted that the binding constant for proteins withmonosaccarides peak at approximately 10⁷ M⁻¹, a remarkable low value forbiological molecular recognition.⁷ This low molecular affinity formonomeric carbohydrates is magnified biologically through what hasbecome known as the “glycoside cluster effect.” This effect ismanifested when carbohydrates are oligomerized, thereby maximizingbinding efficiencies through not only an additive manner but alsothrough entropic means.⁸

X-ray structures of oligosaccharide-binding proteins have revealed thatthe polar groups of the carbohydrates are involved in multiple hydrogenbonding interactions with complementary polar donor and acceptorhydrogen bond sites on the protein. Nature has used this complementaryinteraction to a great extent in order to gain specificity and energyfor binding. Furthermore, numerous salt bridges are observed betweencharged residues on the protein and complementary charged carboxylate,phosphate, sulfate or ammonium functions on the carbohydrate structure.It has been noted that the involvement of serine, tyrosine and threoninehydroxyl groups is relatively uncommon.⁹ It has also been noted thatmost of the complementary non-polar interactions with carbohydratesinvolve aromatic residues on the protein binding partner.¹⁰ Most of thehydrogen bonds involve planar, multivalent side chain groups (Asn, Asp,Glu, Gln, Arg, His). An additional insight was the recognition of theability of 2-aminopyridine moiety to act as a heterocyclic mimetic ofthe asparagines/glutamine amide side chain.¹¹

Several examples of the detailed three-dimensional structure ofpolybasic protein ligands binding to anionic oligosaccharides exist. Thebinding interaction between fibroblast growth factor and heparin¹²reveals that a significant number of positively charged protein residuesinteract with the negatively charged glycoconjugate receptor. It isimportant to recognize that many of the negatively charged species onthe receptor are heterogeneously sulfated on alternating L-iduronic andD-glucosamino sugars.¹³ X-ray analysis of the glycoprotein hormonefollicle-stimulating hormone interacting with its receptor shows that alarge buried interface (2600 Å²) with a high charge density (1.13charges per nm²) defines a universal binding mode where chargecomplementarity defines specificity.¹⁴ Theoretically, a large energybarrier must be overcome by desolvating the partners before binding canoccur.

The carbohydrate-modifying enzymes known as sulfotransferases representan intriguing method used by nature to reversibly create anionic bindingsites on biomolecules. Many literature examples exist of biologicalphenomena such as development, differentiation and especially immunologywhich are modulated by the presence or absence of sulfatedglyco-conjugates.¹⁵ Specifically, the effects of polyamines on bloodcoagulation and fibrinolysis in the presence of glycosaminoglycans(GAGs) has been examined because it is known that heparin (HP) interactswith polyamines, especially with spermine.¹⁶

Recent scientific advances have greatly enabled the ability to delineatethe role of specific carbohydrates in biological processes. Reviews ofthese advances have appeared.^(17,18) An especially exciting developmentis the automated solid-phase synthesis of defined oligiosaccarides.¹⁹The interactions of heparin/heparan sulfate with various proteins havebeen reviewed.²⁰ Screening for inhibitors of oligiosaccharide-mediatedbiological events has been successfully applied to the microtiter plateformat.^(21,22) The use of surface plasmon resonance imaging has beenapplied to the study of protein-carbohydrate interactions.²³ The generaluses of optical biosensors to drug discovery has also been reviewed.²⁴Capillary electrophoresis is an additional tool used to defineinteractions between sulfated polysaccharides and proteins.²⁵

Interruption of carbohydrate-mediated disease processes. A report byJoosten et al. showed that a series of dendritic galabiose compoundscontaining a polyamido core (PAMAM-) had activity in inhibition ofbacterial binding in the subnanomolar concentration levels.²⁶ A reportby Yudovin-Farber showed that anti-prion agents could be produced usingpolycationic oligosaccharides.²⁷ Furthermore, the elimination of prionparticles from infected individuals using polycationic agents has beenshown.²⁸⁻³¹ Medicinal chemistry efforts towards inhibition ofintegrin-mediated events have been made.^(32;33) Molecular recognitionby these cell adhesive molecules known as integrin receptors on the cellsurface is one of the most important biological processes not only incell adhesion but also in fertilization, organ formation, cellmigration, lymphocyte trafficking, immune response, and cancermetastasis.³⁴ Endotoxins, or lipopolysaccharides (LPS), the predominantstructural component of the outer membrane of Gram-negativebacteria,³⁵⁻³⁷ play a pivotal role in septic shock, a syndrome ofsystemic toxicity which occurs frequently when the body's defensemechanisms are compromised or overwhelmed, or as a consequence ofantibiotic chemotherapy of serious systemic infections (Gram-negativesepsis).³⁸⁻⁴¹ Referred to as “blood poisoning” in lay terminology,Gram-negative sepsis is the thirteenth leading cause of overallmortality⁴² and the number one cause of deaths in the intensive careunit,⁴³ accounting for more than 200,000 fatalities in the USannually.⁴⁴ Despite tremendous strides in antimicrobial chemotherapy,the incidence of sepsis has risen almost three-fold from 1979 through2000⁴⁵ and sepsis-associated mortality has essentially remainedunchanged at about 45%⁴⁶, both calling to attention the fact thataggressive antimicrobial therapy alone is insufficient in preventingmortality in patients with serious illnesses, and emphasizing an urgent,unmet need to develop therapeutic options specifically targeting thepathophysiology of sepsis.

The presence of LPS in the systemic circulation causes a widespreadactivation of the innate immune response^(47;48) leading to theuncontrolled production of numerous inflammatory mediators, includingtumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), andinterleukin-6 (IL-6), primarily by cells of the monocyte/macrophagelineage,^(49;50) as well as others, such as nitric oxide produced by theendothelial cell,^(51;52) which, in concert, act to cause a frequentlyfatal systemic inflammatory response,⁵³ termed ‘septic shock’. The toxicmoiety of LPS is its structurally conserved glycolipid component calledLipid A,⁵⁴ which is composed of a hydrophilic, bis-phosphorylateddiglucosamine backbone, and a hydrophobic domain of 6 (E. coli) or 7(Salmonella) acyl chains⁵⁴ (FIG. 1). The pharmacophore necessary for theneutralization of lipid A⁵⁵ by small molecules requires two protonatablepositive charges separated by a distance of ˜14 Å, enabling ionicH-bonds between the cationic groups and the lipid A phosphates; inaddition, appropriately positioned pendant hydrophobic functionalitiesare required to further stabilize the resultant complexes viahydrophobic interactions with the polyacyl domain of lipid A (for arecent review, see Ref.⁵⁶). These structural requisites were firstidentified in certain members of a novel class of compounds, thelipopolyamines, which were originally developed, and are currently beingused as DNA transfection (lipofection) reagents. 57-60 In a detailedstudy of the effect of the hydrocarbon chain length in a homologousseries of acylhomospermines, it was shown that C₁₆ is the ideallipophilic substituent, corresponding to maximal affinity, optimalaqueous solubility (and bioavailability), and neutralization potency.⁶¹

SUMMARY

The present disclosure relates to modulating or interrupting processeswhich comprises binding oligosaccharide-based biomolecules with smallmolecule polycationic agents.

The present disclosure also relates to compounds represented by theformulae:

wherein x is selected from the group consisting of —(CH₂)_(y)—; 1,2-C₆H₄—; 1,3-C₆H₄—; 1,4-C₆H₄—; and —CH₂ OCH₂—;

y is an integer of 0-10;

R is selected from the group consisting of —H, —CH₃, —CH₂C₆H₅,—CH₂-3-indoline, —CH₂-2-indoline, and —CH₂-4-imidazole

m is 0-4;

n is 0-4; and

R′ is selected from the group consisting of —(CH₂)_(o)—CH₃;—(CH₂)_(o)—CH₂NH₂; phenyl; 1-naphthyl and 2-naphthyl;

o is an integer of 0-16;

pharmaceutically acceptable salts thereof; and prodrugs thereof.

The present disclosure also relates to treating diseases of animmunological disorder such as psoriasis, lupus, Crohn's disease,inflammatory bowel disease, rheumatoid arthritis, Type 1 diabetes, Type2 diabetes or sepsis by administering to a patient in need thereof, aneffective amount of a compound disclosed above.

A further aspect of this discloses is concerned with treating diseasesof an infectious disorder such as those caused by bacteria, fungi orviruses by administering to a patient in need thereof, an effectiveamount of a compound disclosed above.

SUMMARY OF DRAWINGS

FIG. 1 shows a schematic and crystal structure of lipopolysaccharidealong with Lipid A.

FIG. 2 illustrates the bimodal distribution of binding affinities.

FIG. 3 illustrates an energy-minimized model of the disclosedscaffold-lipid A complex.

FIG. 4 illustrates ability of compounds of the disclosure to inhibit NOproduction.

FIG. 5 illustrates the correlation of binding affirmative toneutralization patterning.

DESCRIPTION OF BEST AND VARIOUS MODES

Compounds of the present disclosure are represented by the followingformulae:

wherein x is selected from the group consisting of —(CH₂)_(y)—;1,2-C₆H₄—; 1,3-C₆H₄—; 1,4-C₆H₄—; and —CH₂ OCH₂—;

y is an integer of 0-10;

R is selected from the group consisting of —H, —CH₃, —CH₂C₆H₅,—CH₂-3-indoline, —CH₂-2-indoline, and —CH₂-4-imidazole

m is 0-4;

n is 0-4; and

R′ is selected from the group consisting of —(CH₂)_(o)—CH₃;—(CH₂)_(o)—CH₂NH₂; phenyl; 1-naphthyl and 2-naphthyl;

o is an integer of 0-16;

pharmaceutically acceptable salts thereof; and prodrugs thereof.

Preferred compounds according to the present disclosure are representedby the following formulae:

1. formula for MQTS 1172:

2. formula for MQTS 1132:

3. The formula for MQTS 1007:

4. The formula for MQTS 1242:

Further preferred compounds, representing 1,3-C₆H₄- moleculararrangement as specified above, according to the present disclosure arerepresented by the following formulae:

According to the present disclosure a terminally-placed long-chainaliphatic group is important for effective LPS neutralization.Furthermore, the chemical space defined by the described compoundsidentify novel, non-polyamine scaffolds that incorporate the LPS-bindingpharmacophore described above.

Prodrug forms of the compounds bearing various nitrogen functions(amino, hydroxyamino, hydrazino, guanidino, amidino, amide, etc.) mayinclude the following types of derivatives where each R groupindividually may be hydrogen, substituted or unsubstituted alkyl, aryl,alkenyl, alkynyl, heterocycle, alkylaryl, aralkyl, aralkenyl, aralkynyl,cycloalkyl or cycloalkenyl groups as defined above.

-   Carboxamides, —NHC(O)R-   Carbamates, —NHC(O)OR-   (Acyloxy)alkyl Carbamates, NHC(O)OROC(O)R-   Enamines, —NHCR(═CHCRO₂R) or —NHCR(═CHCRONR₂)-   Schiff Bases, —N═CR₂-   Mannich Bases (from carboximide compounds), RCONHCH₂NR₂    Preparations of such prodrug derivatives are discussed in various    literature sources (examples are: Alexander et al., J. Med. Chem.    1988, 31, 318; Aligas-Martin et al., PCT WO pp/41531, p.30). The    nitrogen function converted in preparing these derivatives is one    (or more) of the nitrogen atoms of a compound of the invention.

Prodrug forms of carboxyl-bearing compounds of the invention includeesters (—CO₂R) where the R group corresponds to any alcohol whoserelease in the body through enzymatic or hydrolytic processes would beat pharmaceutically acceptable levels.

Another prodrug derived from a carboxylic acid form of the invention maybe a quaternary salt type

of structure described by Bodor et al., J. Med. Chem. 1980, 23, 469.

It is of course understood that the compounds of the present disclosurerelate to all optical isomers and stereo-isomers at the various possibleatoms of the molecule.

The compounds of this disclosure form acid and base addition salts witha wide variety of organic and inorganic acids and bases and includes thephysiologically acceptable salts which are often used in pharmaceuticalchemistry. Such salts are also part of this disclosure. Typicalinorganic acids used to form such salts include hydrochloric,hydrobromic, hydroiodic, nitric, sulfuric, phosphoric, hypophosphoricand the like. Salts derived from organic acids, such as aliphatic monoand dicarboxylic acids, phenyl substituted alkonic acids,hydroxyalkanoic and hydroxyalkandioic acids, aromatic acids, aliphaticand aromatic sulfonic acids, may also be used. Such pharmaceuticallyacceptable salts thus include acetate, phenylacetate, trifluoroacetate,acrylate, ascorbate, benzoate, chlorobenzoate, dinitrobenzoate,hydroxybenzoate, methoxybenzoate, methylbenzoate, o-acetoxybenzoate,naphthalene-2-benzoate, bromide, isobutyrate, phenylbutyrate,β-hydroxybutyrate, butyne-1,4-dioate, hexyne-1,4-dioate, cabrate,caprylate, chloride, cinnamate, citrate, formate, fumarate, glycollate,heptanoate, hippurate, lactate, malate, maleate, hydroxymaleate,malonate, mandelate, mesylate, nicotinate, isonicotinate, nitrate,oxalate, phthalate, teraphthalate, phosphate, monohydrogenphosphate,dihydrogenphosphate, metaphosphate, pyrophosphate, propiolate,propionate, phenylpropionate, salicylate, sebacate, succinate, suberate,sulfate, bisulfate, pyrosulfate, sulfite, bisulfite, sulfonate,benzene-sulfonate, p-bromobenzenesulfonate, chlorobenzenesulfonate,ethanesulfonate, 2-hydroxyethanesulfonate, methanesulfonate,naphthalene-1-sulfonate, naphthalene-2-sulfonate, p-toleunesulfonate,xylenesulfonate, tartarate, and the like.

Bases commonly used for formation of salts include ammonium hydroxideand alkali and alkaline earth metal hydroxides, carbonates, as well asaliphatic and primary, secondary and tertiary amines, aliphaticdiamines. Bases especially useful in the preparation of addition saltsinclude sodium hydroxide, potassium hydroxide, ammonium hydroxide,potassium carbonate, methylamine, diethylamine, and ethylene diamine.

The compounds may be utilized alone or in combination with other agents.

In another aspect of the disclosure, compositions containing the abovedescribed compounds and derivatives are provided. Typically, thecompositions are formulated to be suitable for pharmaceutical use by theinclusion of appropriate carriers or excipients.

In a further aspect of the disclosure methods for the use of the abovedescribed compounds, as well as compositions, are provided. Thesemethods include uses of the invention's compounds to modulate orinterrupt biological processes involving the recognition or binding ofoligosaccharides-based biomolecules. Compounds of the present disclosureare useful for treating a disease or condition in which the inhibitionof NO (nitric oxide) is desirable. Examples of human diseases andconditions include, but are not limited to, chronic or acuteinflammation, inflammatory bowel disease (including Crohn's disease),inflammatory bowel syndrome, autoimmune diseases rheumatoid arthritis,systemic lupus erythematosus, cutaneous forms of lupus, Type 1 and Type2 diabetes, multiple sclerosis, psoriasis, spondyloarthropathies (SpA)including spondylitis, synovitis, psoriatic arthritis and subclinicalgut inflammation and infectious diseases including sepsis, septic shock,endotoxic shock, HIV and other viral infections includingcytomegalovirus, herpes simplex virus, influenza virus; infectiousdisorders caused by bacteria or fungi.

As discussed above, the present disclosure describes an example of amethod to selectively interrupt oligosaccharide-mediated biologicalphenomenon. The method recognizes the exhaustive number of potentialbiological and drug targets involving oligosaccharide conjugates. Themolecular contributions for binding to lipid A/endotoxin, one of anumber of these anionic oligosaccharide targets, were assessed in arapid and detailed fashion through the application of a prospectivelydesigned, moderately-sized 540-membered example library. Analysis of thecontribution that each individual monomeric library component made tothe most tight-binding analogs was facilitated by use of “molecularvector analysis.” This analysis confirmed the importance of thelipophilic long chain aliphatic group (typically C₁₂ to C₂₂ lipid chainand more typically C₁₈ lipid chain), while also pointing to thecontribution made by heteroaromatic moieties such as indole portion oftryptophan. The incorporation of techniques such as Synphase lanternstogether with the data transfer/handling software made synthesis of themulti-hundred membered library much more straightforward.

The following non-limiting examples are presented to further illustratethe present disclosure.

General experimental methods. The sources of all chemical reagents andstarting materials are of the highest grade available and are usedwithout further purification. Lanterns used are Mimotopes SynPhase PSD-Series Lanterns™ with a trityl alcohol linker. Thin-layerchromatography analysis and column chromatography is performed usingMerck F₂₅₄ silica gel plates and Baker 40 μm flash chromatographypacking, respectively. TLC analysis used the specified solvent systemswith detection by ninhydrin staining. Data handling is facilitated bythe use of BalanceLink V3.0 software from Mettler-Toledo to enabletransfer of weight values directly into an Excel spreadsheet. Solventsfrom resin cleavage are removed through the use of a Savant centrifugalevaporator operating at 25° C.

LC/MS analyzes are performed using a Gilson 322 HPLC system coupled to a215 liquid handler. Detection was by a Finnigan AQA operating in ESI⁺mode (m/z range 140 to 1600 amu) together with an Agilent 1100 seriesdiode array detector (UV range 220 to 320 nm). Gradient elution from 2to 7 min. at 0.2 mL/min. is performed using 2% to 100% CH₃CN in H₂O(both with 0.05% TFA) using a Waters XTerra MS C₁₈ 2.1×150 mm (3.5 μm)column. ¹H NMR spectra are recorded at 300 MHz on a Bruker AV300spectrometer at the University of Washington, Seattle. ¹H NMR signalsare generally multiples unless otherwise noted as s=singlet, d=doublet,t=triplet or m=multiplet. Chemical shifts are relative to external3-(trimethylsilyl)-1-propanesulfonic acid, sodium salt.

EXAMPLE 1

Ethyl N-(2-nitrophenylsulfonamide)-glycinate (2a)—To a solution of 25.11g (0.180 mole) of ethyl glycinate hydrochloride and 42.11 g (0.190 mole,1.06 eq) of 2-nitrophenylsulfonylchloride in 400 mL of dry CH₂Cl₂ at 0°C. is added 76.6 mL (0.44 mole, 2.44 eq) of ^(i)Pr₂NEt dropwise. Theresulting solution is stirred for 18 h when it is quenched by theaddition of 200 mL of H₂O. The organic layer is removed and the aqueouspart is re-extracted by an additional portion of 200 mL CH₂Cl₂. Thecombined organic layers are washed with 0.1 N HCl then brine and driedand evaporated to give the crude product as an off-white solid. This iscrystallized from 400 mL of abs. EtOH to give 44.69 g (90%) whitecrystals. ¹H NMR (CDCl₃, δ): 8.16 (d, 1H), 7.82 (d, 1H), 7.78 (m, 2H),5.62 (s, 1H), 4.04 (q, 2H), 3.98 (s, 2H), 1.24 (t, 3H).

EXAMPLE 2

Ethyl N-(2-nitrophenylsulfonamide)-2-aminopropionate (2b)—Using theprocedure described above this product is produced in 80% yield. ¹H NMR(CDCl₃, δ): 8.24 (d, 1H), 7.81 (d, 1H), 7.74 (m, 2H), 5.75 (s, 1H), 4.11(q, 2H), 3.43 (q, 2H), 3.23 (m, 2H), 2.43 (t, 2H), 1.22 (t, 3H).

EXAMPLE 3

Ethyl N-(2-nitrophenylsulfonamide)-3-aminobutyrate (2c)—Using theprocedure described for 2a, this product is produced in 54% yieldfollowing crystallization from abs. EtOH. ¹H NMR (CDCl₃, δ): 8.21 (d,1H), 7.84 (d, 1H), 7.77 (m, 2H), 5.65 (s, 1H), 4.09 (q, 2H), 3.42 (q,2H), 3.23 (m, 2H), 2.43 (t, 2H), 1.91 (m, 2H), 1.25 (t, 3H).

EXAMPLE 4

General alkylated monomer synthesis - Mitsunobu alkylation: EthylN-2-(1-naphthyl)ethyl-(2-nitrophenylsulfonamide)-2-aminopropionate(3b1)—To the solution produced by dissolving 3.02 g (10 mmol) of 2b,1.72 g (10 mmol) of 2-(1-naphthyl)-ethanol and 3.98 g (15 mmol) oftriphenylphosphine in 50 mL of dry CH₂Cl₂ is added dropwise at 25° C. asolution of 2.95 mL (15 mmol) of diisopropylazodicarboxylate in 15 mL ofdry CH₂Cl₂. The resulting yellow colored solution is stirred for 16 hwhen the reaction solution is diluted in 75 mL CH₂Cl₂ and 75 mL 0.1NHCl. The aqueous layer is removed and re-extracted by an additional 75mL portion of CH₂Cl₂. The combined organic layers are washed with brine,dried and evaporated to give the crude product as a yellow oil. Columnchromatography over silica gel uses 3:1 hexane/ethyl acetate to give2.17 g (48% yield) colorless crystals.

EXAMPLE 5

Ester hydrolysis:N-2-(1-naphthyl)ethyl-(2-nitrophenylsulfonamide)-2-aminopropionic acid(4b1)—To the clear solution of 3.17 g (6.9 mmol) of 3b1 in 100 mL of THFis added 13.9 mL (2 eq) of 2N LiOH in H₂O. The resulting two-phasemixture is vigorously stirred for 16 h when the THF is evaporated invacuo and the resulting residue is suspended in 75 mL CH₂Cl₂ and 50 mLof IN HCl. The aqueous part is re-extracted by an additional portion of75 mL CH₂Cl₂ and the combined organic layers are dried and evaporated togive oily solids. When TLC analysis using 1:1 hex/EtOAc withI₂-detection shows the presence of diisopropylhydrazine side-productcolumn chromatography with 8:2 hex/EtOAc can be used to obtain purecarboxylic acid monomer material.

15-Membered test library production. A set of 15 Mimotopes SynPhase PSD-Series Lanterns™ with a trityl alcohol linker (15×35 μmol=0.525 mmoltotal) are labeled with spindles and cogs and dried under high vacuumover P₂O₅ for 18 h. They are then suspended in a solution of 18 mL dryCH₂Cl₂ and 2 mL of acetyl chloride. Following gentle shaking for 3.5 hthe lanterns are washed three times with dry CH₂Cl₂ to give P1. Whilestill in their CH₂Cl₂ swollen form they are suspended in 20 mL of dryCH₂Cl₂ and 5 mL of 3-aminopropanol is added. The vessel is shaken for 18h then washed three times each with CH₂Cl₂, DMF, ^(i)PrOH, THF andCH₂Cl₂ (standard washing sequence) then is dried under high vacuumgiving P2.

The lanterns are next transformed into their amine form (P4) by thefollowing two-step sequence. Suspension in 20 mL dry CH₂Cl₂ is followedby the addition of 0.39 g (2.63 mmol, 5 eq) of phthalimide and 0.69 g (5eq) of triphenylphosphine as solids. The reaction vessel is shaken todissolve these reagents then treated portionwise with a solution of 0.52mL of diisopropyldiazodicarboxylate dissolved in 10 mL of dry CH₂Cl₂.This vessel is shaken for 3 h when standard washing and drying givelanterns P3. These are suspended in 10 mL of abs. EtOH and treated with10 mL of hydrazine hydrate. The vessel is tightly capped then heated to60° C. in a rotating oven for 18 h. Following cooling to roomtemperature the lanterns are washed and dried in standard manner to givelantern form P4.

Fmoc-amino acid couplings use the following standard conditions forproduction of lanterns P5. The amino lanterns P4 are suspended andswelled in 5 mL of dry DMF. A solution containing 1.02 g (2.63 mmol, 5eq) of Fmoc-Phe-OH, 1.0 g (5 eq) of HBTU, 0.2 g (2.5 eq) of HOBt and0.92 mL (10 eq) of ^(i)Pr₂NEt is prepared and shaken for 10 min prior toaddition to the lanterns suspended above. The resulting reaction mixtureis shaken gently for 2 h when standard washing and drying give theproduct lanterns P5. The peptide coupling and resin loading of thelanterns is measured by dilution of the solution from next, Fmoc-groupremoval reaction. The lanterns are suspended in 15 mL 20% piperidine inDMF and shaken for 15 min. A 0.10 mL aliquot is removed and diluted to10 mL in the same solvent mixture. Following solvent zeroing a UVmeasurement of the absorbance at 301 nm gives a value of 1.186. Usingthe ε_(a) value for Fmoc-piperidine adduct of 14102 L mol⁻¹ cm⁻¹ aloading efficiency of 16.7 μmole or 48% is calculated (1.186×14102=16.7)(Manufacturer's stated loading was 35 μmole). Standard washing anddrying of the lanterns following a 1.5 h reaction time gives lanternsP6.

These lanterns are now used to couple, individually, to each of the 15monomers synthesized through the process described above. Fifteen 4 mLdried vials are loaded with 0.066 g (0.14 mmol, 4 eq based on an avg MWof 474.4) of each monomer. One mL of a solution that is preparedcontaining 0.80 g (2.1 mmol, 4×15 eq) of HBTU, 0.16 g (1.05 mmol, 2×15eq) of HOBt and 0.732 mL (4.2 mmol, 8 eq) of ^(i)Pr₂NEt in 15 mL of dryDMF is added to each monomer containing vial. These vials are gentlyshaken while the lanterns are pre-swelled together in 15 mL of dry DMF.After 10 min each labeled lantern is placed into its respective vialcontaining the activated monomer ester. The lanterns are shakenovernight then the reaction solution is decanted. They are combined andwashed in standard fashion. Drying gaies the protected lanterns P7. TheNPS group is removed by treating the combined set of lanterns with 5 mLof 2-mercaptoethanol, 5 mL of DBU and 15 mL of DMF for 18 h. Standardwashing and drying gives the loaded resins P8 ready for cleavage.

Each lantern is placed in an individually marked and pre-tared 4 mL vialand treated with 2.0 mL of cleavage cocktail consisting of 80:18:2CH₂Cl₂/TFA/^(i)Pr₃SiH for 1 h. The lanterns are extracted with tweezersand washed with CH₂Cl₂ and the cleavage solutions are evaporated. Theresulting yellow oil residues are each dissolved in 0.50 mL MeOH and 20μL removed and diluted to 200 μL in H₂O for LC/MS analysis. LC/MS isperformed on all fifteen analogs. The concentrated stock MeOH solutionsare also used for TLC analysis in two solvent systems: a) 8:2CH₃CN/concd NH₄OH; b) 90:8:2 CHCl₃/MeOH/concd NH₄0H. ¹H NMR is performedon two analogs below.

MQTS 1093T—LC/MS calcd [M+H] for C₂₇H₃₂N₄O₂: m/z 445; obsd 445 at 13.6min. ¹H NMR (D₂O, δ): 7.73-7.16 (m, 14H), 4.38 (t, 1H), 4.22 (m, 2H),3.84 (m, 2H), 3.32-2.83 (m, 2H), 2.60 (m, 2H), 2.02 (m, 2H), 1.60 (m,2H).

MQTS 1095T—LC/MS calcd [M+H] for C₁₇H₂₉N₅O₂: m/z 336; obsd 336 at 12.9min. ¹H NMR (D₂O, δ): 7.38-7.20 (m, 5H), 4.51 (t, 1H), 3.86 (m, 2H),3.30-3.15 (m, 2H), 3.06 (t, 8H), 2.02 (m, 2H), 1.62 (m, 2H).

540-Membered example library production. Synthesis of the complete540-membered library follows the same sequence as that for the 15-membered test library. 540 lanterns are labeled with spindles and cogsand are activated to their P1 forms using the procedure above. Six setsof 90 lanterns are sorted into individual vessels and are treated with10 g (or 10 mL) of the amino alcohol shown in Chart 1. Followingreaction and washing to give their P2 forms the 540 lanterns arere-combined and converted to their free amine form via the sequenceoutlined above (P2 to P4). The lanterns are then split into six groupswith 90 members and coupled to the requisite Fmoc-amino acid using theprocedure outlined above. UV analysis of the Fmoc-loading of sixrandomly selected lanterns showed respectable 60-125% loadingefficiencies. Following couplings the re-combined lanterns are treatedwith 20% piperidine/DMF as above to give the free-amine form P6lanterns. The lanterns are then split (36×15) for their final couplingreaction to the 15 monomers 4 using the standard coupling conditions.NPS-protecting group cleavage readies the lanterns for sorting into 540individual pre-tared 4 mL vials. Final cleavage gives the crude analogsMQTS 1001 to 1540 in their TFA salt forms. An average yield of 84% iscalculated based on the expected structure and excluding thosewith >200% yield (n=36).

The entire library is characterized by TLC and LC/MS. The crude materialis mostly dissolved in 1.0 mL of MeOH and spotted onto TLC plates. Ifinsoluble particles remain they are removed by filtration prior tochemical or biological characterization. Elution of the plates use thesolvent system CHCl₃/MeOH/concd NH₄OH 85:13:2 with ninhydrin detection.The above concentrated stock solutions are diluted 20× into 1% TFA inH₂O for LC/MS analysis. The MeOH sample solutions are treated with 1.0mL of 6N HCl then evaporated to give the HCl salts of the finalproducts. These are dissolved in the amount of 20% DMSO/H₂O that isrequired to give 20 mM solutions based on the crude yields that areobtained. The use of an Excel spreadsheet with the pretared and finalvial weights together with MQTS number, structures, molecular formula,and molecular weights of free bases imported from ISIS base greatlyfacilitate the calculations of salt molecular weights, percent yieldsand amount of solvent necessary to give bioscreening solutions.

Rationale and design of molecular scaffold and library monomers. Thedesign of the example 540-membered library is to: i) to confirm andvalidate the lipid A binding pharmacophore in compounds withnon-polyamine scaffolds; ii) to maximize diversity of library memberswithin this context; iii) to systematically test the hypotheses that theintroduction of aromatic groups and/or H-bond donor/acceptor atoms inthe scaffold enhance binding affinity. Several potential strategies toenhance carbohydrate-binding affinity are used by targeting additionalinteractions with the diglucosamine backbone of lipid A. Both covalent(such as by using boronates which form esters with the vicinal cisdiols)^(62;63) as well as noncovalent interactions^(64;65) areconsidered. An examination of the Protein Data Bank for lectin-sugarcomplexes^(66;67) as well as relevant literature⁶⁸⁻⁷⁰ point to (a)multiple H-bond donor/acceptor pairs contributing to the enthalpy ofbinding and (b) an unusual preponderance of aromatic side chains aroundthe sugar binding site,⁶⁶ suggesting either multiple CH-π^(71;72) orOH-π weak H-bonds.^(73;74) Indeed, a lipid A receptor with aoligocyclopentane backbone substituted with amino and indolefunctionalities has been described.⁷⁵ A recent report describedLPS-targeting peptoids isolated from a positional scanning library whichincorporated various aromatic constituents along its backbone.⁷⁶Furthermore, the crystal structure of LPS indicates a range ofinter-atomic distances between 2.4-4 Å between H-bond donor/acceptoratoms on the lipid A backbone (see FIG. 1).⁷⁷ Library members aretherefore designed with an intervening distance of 2-3 carbon bondsbetween H-bond donor/acceptor atoms in order to favor complementaritywith the anionic carbohydrate target.

The scaffold and elements (PORTIONS 1-3) of the combinatorial libraryare shown in Chart 1. The distance between the terminal amines are‘dialed in’ by varying intervening elements in both PORTION 1 as well asthe Gly/Ala/GABA amino acids in PORTION 3. As can be seen in Chart 1,PORTION2 contains a preponderance of aromatic groups. In PORTION 3.y,both aliphatic and aromatic substituents are incorporated in order tomeet the requirement of a long-chain aliphatic group for optimalactivity.⁶¹

Synthesis of library monomers. Using a Mitsunobu-mediated alkylation ofsolid-phase 2-nitrophenylsulfonamides^(78;79) is initially considered,but during the formation of the requisite resin-bound sulfonamides tocompletion is not achieved. Similar difficulties using this approach onsolid-phase have been previously reported in the literature.⁸⁰ Asolution-phase alkylation of the esters of amino-acid sulfonamides forthe synthesis of the fifteen PORTION 3 monomers en route to thesynthesis of the 540-membered library by the route depicted in Scheme 1is instead employed. Modification of the conditions by the use of themore hindered base ^(i)Pr₂NEt enables the desired sulfonamides to beprepared in good yield following crystallization.

Alkylation of each of the three sulfonamides by the five primaryalcohols corresponding to the PORTION 3 substituents shown in Chart 1proceeds in straightforward fashion. Following column chromatographypurification some of these alkylated ester-sulfonamides show thepresence of various amounts of an impurity corresponding todiisopropylhydrazinedicarboxylate, a side-product from the Mitsunobualkylation. This material can be eliminated either at this estermaterial step (3a-c) or in the next, carboxylic acid step (4a-c) bycolumn chromatography. In either case, the impurity is readily detectedby TLC using I₂ staining or by ¹H NMR, ensuring its complete removal inthe products. Hydrolysis of the esters is accomplished in astraightforward manner. All molecules show high purity by TLC and ¹H NMRwith their identities being confirmed by LC/MS analysis.

Chemical route to library: Fifteen-membered test library. A test of thesolid-phase synthetic route is carried out using each of the fifteenmonomers produced above attached to fifteen identical lanternscontaining the 1,3-diaminopropane-Phe PORTION 1:PORTION 2 resin partner(Scheme 2). Prior experience with symmetrical diamine attachment totritylchloride solid-phase resin shows that significant crosslinkingoccurs leading to substantial diamine contamination in the cleavedproducts. For this reason a three-step sequence is used involvingattachment of an amino alcohol followed by —OH to —NH₂ conversion.Mitsunobu-mediated phthalimide group attachment followed by hydrazineliberation of the free amine gives the desired lanterns. This processcompletely eliminates the formation of the diamine side-product whilesubstantially increasing the loading efficiency of the desired product.

Standard peptide coupling conditions are used to add the Phe residue tothis set of lanterns. UV analysis of the liberated Fmoc group from thenext step shows a loading efficiency of 48% at this stage. The lanternsare then individually attached to each of the fifteen monomers usingHBTU coupling conditions. The NPS-groups are removed using2-mercaptoethanol/DBU/DMF. The products are then cleaved using 80:18:2CH₂Cl₂/TFA/^(i)Pr₃SiH directly into individual pre-tared 4 mL vials.Data handling is facilitated by direct data acquisition from theweighing balance into a spreadsheet program. In this way, dataassociated with the samples including vial tare weight and net crudeweight can be coordinated with the sample ID number, structure,molecular weight, theoretical yield, and crude percent yield. Thesamples are dissolved in MeOH and sampled for TLC and LC/MS analyses asdescribed below. These crude samples are then treated with an equalvolume of 6N HCl and evaporated to give their per-HCl salts. For thefifteen test samples an average weight percent yield of 70% iscalculated represented by an average crude weight of 18.4 mg.

TLC and LC/MS analysis of the crude samples support the viability of the8-step process. Several informative observations are made following thisanalysis: 1) Side-products with masses at 147 amu lower m/z values areobserved. Two major spots are seen in the TLC analysis of most of thesetest analogs and a side-peak showed up at a shorter retention times inthe LC/MS chromatograms. It is deduced that these side-products aregenerated from the incomplete coupling of the Phe-PORTION 2 residue. Itis concluded that this lower than desired Phe loading gives rise tosubstantial amounts of truncated products in the samples and may explainthe lower than expected 48% loading efficiency measured following thisstep. 2) Alkene addition products are observed with the unsaturatedPORTION 3.x4 monomers. A mixture of un- and mono-substituted TFA-adductsare seen. Subsequent analysis of the HCl salts showed complete exchangeof ⁻OTFA by ⁻Cl. By carrying out a test library synthesis it is reasonedthat PORTION 2 loading conditions should be modified to decreasetruncated side-product formation. Furthermore, it is determined that thecleavage conditions do not completely eliminate side-product formationinvolving acid-mediated alkene addition.

Synthesis of 540-membered example library. A coding system is devised tolabel the lanterns and the entire library's structures are enumeratedinto an ISIS™ database. A spreadsheet is configured for handling thedata generated. Library production follows the route outlined in Scheme2 and utilizes the components shown in Chart 1. A large excess of thesix amino alcohols is used to elaborate 90 labeled lanterns in sixindividual vessels. The lanterns are then recombined for the nexttwo-step —OH to —NH₂ conversion. Splitting and sorting enable the nextPORTION2 components to be added. The number of equivalents of Fmoc-aminoacid used in this step is increased from 4 to 5 in order to decrease theamount of incomplete addition products. The loading is improved by UVanalysis of the liberated Fmoc-piperidine adduct from a selection ofindividual lanterns with different PORTION 1: PORTION2 components. Anaverage loading of 109% (relative to the manufacturer's value of 35μmole) is obtained.

The Fmoc-groups are removed from the entire library and the monomer setis coupled to fifteen sets of 36 lanterns each. The NPS-grouping isremoved and the lanterns are sorted into individual pre-tared vials inpreparation for final cleavage. Cleavage occurs in similar fashion tothat described above and gives an average of 84% yield of thehydrochloride salt of the crude products. TLC and LC/MS analysis of theentire set of compounds show adequate purity for the majority of thelibrary and confirmed that each contain the desired product as the majorcomponent. Side-products due to truncated PORTION 2 addition are absentbut acid-mediated addition products to some alkene containing productsis still observed. The crude library is dissolved in 20% DMSO/H₂O at 20mM and is screened in the assays described below.

Quantitative Estimation of LPS Binding Affinity. The relative bindingaffinities of the entire library of analogs with a recently-describedhigh-throughput fluorescence based displacement assay, is examined usingBODIPY-TR cadaverine (BC).^(81;82) Results are reported as half-maximaleffective displacement of probe (ED₅₀). In all experiments, Polymyxin B(PMB), a decapeptide antibiotic, known to bind and neutralize LPS,⁸³⁻⁸⁶is used as a reference compound.

As shown in FIG. 2, a distinct biphasic distribution of bindingaffinities can be observed, with a clear demarcation of high- andlow-affinity compounds. A particularly instructive method of graphicalevaluation of library screening results is shown in FIG. 3. Thismethodology is referred to herein as ‘molecular vector analysis’; and itinvolves counting the number of occurrences of each individual monomerin the subset of analogs in the top binders (52 analogs with ED₅₀<10μM), and the frequency of monomers in weak-binding compounds (488analogs with ED₅₀>10 μM). The resulting histograms are easy tointerpret, and simple statistical analyses (χ-square) can be employed toverify the importance of those building blocks that contribute most tothe resulting binding.

The most profound effects on activity appear with the selection of longchain hydrophobic C₁₈ chain (PORTION 3.x.2) and by the selection of anindole moiety (Trp) in the PORTION 2 position. More subtle, albeit noless important, insights can be gleaned from the observations madeconcerning selection of PORTION 1 and PORTION 3 monomers. It wouldappear that the original concept of “distance dialing”^(61;82;87;88)designed into the library play a role in the results observed. Theincorporation of PORTION 1 monomer 1,3-diaminopropane gives anunexpectedly high population of members in the top 52 samples. Likewise,selection of 2-aminopropionic acid for PORTION 3.B lead to a highernumber of tight binders than the other two monomer components. Based onprior work,^(61;82;88-90) this is attributed to a better congruence inthe distance between the two terminal protonatable nitrogen atoms inthis subset of analogs and that between the anionic phosphates on thelipid A backbone, enabling effective ionic H-bonds between the chargedgroups. It is therefore instructive to construct the “best” scaffoldusing the optimal PORTION 1 “vector” component 1,3-diaminopropane, Trpin PORTION 2, and a PORTION 3 bearing a C₁₈ alkyl group. The backbone ofthis molecule (without the C₁₈ alkyl chain) is then docked on a crystalstructure-derived^(77;91) model of lipid A using AutoDock^(92;93). Thealkyl chain is omitted in the modeling since it has previously beenobserved that the force fields within AutoDock do not adequately reflecthydrophobic interactions for glycolipids, such as lipid A. In theenergy-minimized model of the docked scaffold-lipid A complex, (FIG. 3),a distance of 14.7 Å is observed between the terminal amines, matchingvery closely the previously determined optimized distance betweenprotonatable amine groups in LPS binders.^(55;82;88;90) The O atoms onthe lipid A phosphates are also found to be within H-bonding distancesof the amines (FIG. 3). Other PORTION 1 monomer components such as thosecomposed of 1,5-diaminopentane, significantly diverge from the optimalvalue and consequently do not bind LPS as well (FIG. 2).

Re-synthesis of active molecules. Based on the combination of resultsfrom the binding and preliminary NO inhibition assays, a series of 25analogs is selected for re-synthesis and purification (Table 1). Inorder to provide enough material for purification, we used two lanternsare used for each individual analog. As previously seen in the fifteentest-analog series, minor amounts of truncated (-PORTION 2 amino-acid)species are seen with several of these examples. It is possible toisolate 9 molecules representing these truncated analogs (Table 1). Thesame synthetic route is used as before and the crude products arepurified over 900 mg disposal SiO₂ solid-phase extraction columns. Thesepurified analogs show greater than 90% purity when analyzed by TLC andLC/MS methods. Table 1 shows the MQTS numbers, structures and BC-bindingdata (ED₅₀ values) together with NO inhibition data (IC₅₀ values).

Assessment of neutralization of LPS toxicity: NO inhibition activity.Murine monocytes (J774.A1 cells) produce measurable quantities of NOupon exposure to LPS and provide a high-throughput and validated modelfor the rapid and quantitative assessment of compounds in neutralizingthe toxicity of LPS.^(81;82;94) Compounds that neutralize LPS inhibit NOproduction in a dose-dependent manner from which 50% inhibitoryconcentrations (IC₅₀) were determined (FIG. 4). The analogs determinedto have the highest affinity in the BC-binding assay are then assayed inthis NO inhibition assay (Table 1). Results in this assay parallel thosein the binding assay (FIG. 5).

Hit re-synthesis and characterization. Two lanterns per analog are usedto resynthesize the analogs shown in Table 1. Synthesis follow theprocedures given above. The resulting crude products in their TFA saltforms are purified over disposable Alltech SPE cartridges containing 900mg of SiO₂. Chromatography uses 5 to 20% MeOH in CH₂Cl₂ with 1% concdNH4OH. TLC solvent is 80:18:2 CH₂Cl₂/MeOH/concd NH4OH with detection byninhydrin. The product containing fractions are pooled and evaporatedthen converted to their per-HCl salt forms by treatment with 6N HCl inMeOH and re-evaporation. In several cases shown in Table 1, truncatedanalogs (MQTS 2322-2330) without the internal amino acid portion arealso isolated from these products. Purified samples are analyzed by ¹HNMR, TLC and LC/MS using the methods described above. A selection ofLC/MS and NMR data is given here. Yields for these products range from 6to 25% following the 8-step solid-phase route and all show over 90%purity by the methods noted.

MQTS 1002—2.9 mg (6% yield) white solid is obtained. LC/MS calcd [M+H]for C₃₃H₆₀N₄O₃: m/z 562; obsd 562 at 14.2 min. ¹H NMR (D₂O, δ):7.35-6.92 (m, 5H), 3.86 (m, 1H), 3.68 (m, 2H), 3.57 (m, 2H), 3.39 (m,4H), 3.14 (m, 4H), 2.98 (m, 2H), 1.63 (m, 2H), 1.17 (s, 30H), 0.80 (s,3H).

MQTS 1007—5.3 mg (12% yield) white solid is obtained. LC/MS calcd [M+H]for C₃₄H₆₂N₄O₃: m/z 575; obsd 575 at 14.7 min. ¹H NMR (D₂O, δ):7.38-6.97 (m, 5H), 4.56 (m, 1H), 3.63 (t, 2H), 3.48 (m, 2H), 3.31 (m,2H), 3.14 (m, 4H), 2.83 (m, 2H), 2.60 (m, 4H), 1.42 (m, 2H), 1.18 (s,30H), 0.82 (t, 3H)

MQTS 1012—3.6 mg (8% yield) white solid is obtained. LC/MS calcd [M+H]for C₃₅H₆₄N₄O₃: m/z 590; obsd 590 at 14.7 min. ¹H NMR (D2O, δ):7.36-6.94 (m, 5H), 4.58 (m, 1H), 3.63 (m, 2H), 3.52 (m, 2H), 3.32 (m,2H), 3.11 (m, 4H), 2.55 (m, 2H), 2.28 (m, 2H), 1.63 (m, 2H), 1.50 (m,2H), 1.17 (s, 32H), 0.80 (t, 3H).

MQTS 1032—6.3 mg (14% yield) white solid is obtained. LC/MS calcd [M+H]for C₃₀H₅₈N₆O₃: m/z 552; obsd 552 at 13.0 min. ¹H NMR (D₂O, δ): 8.53 (s,1H), 7.28 (s, 1H), 3.93 (s, 1H), 3.63 (t, 2H), 3.48 (m, 2H), 3.32 (m,2H), 3.11 (m, 4H), 3.01 (m, 2H), 1.66 (m, 2H), 1.20 (s, 32H), 0.79 (t,3H).

MQTS 1037—5.7 mg (13% yield) white solid is obtained. LC/MS calcd [M+H]for C₃₁H₆₀N₆O₃: m/z 566; obsd 566 at 12.9 min. ¹H NMR (D₂O, δ): 8.58 (s,1H), 7.26 (s, 1H), 4.58 (t, 1H), 3.63 (s, 2H), 3.47 (t, 2H), 3.28 (m,2H), 3.31 (m, 2H), 3.12 (m, 4H), 2.98 (m, 2H), 2.78 (m, 2H), 1.65 (m,2H), 1.20 (s, 30H), 0.78 (t, 3H).

MQTS 1042—8.1 mg (18% yield) white solid is obtained. LC/MS calcd [M+H]for C₃₂H₆₂N₆O₃: m/z 580; obsd 580 at 12.9 min. ¹H NMR (D20, 6): 8.61 (s,1H), 7.27 (s, 1H), 4.58 (t, 1H), 3.63 (t, 2H), 3.49 (m, 2H), 3.32 (m,2H), 3.13 (m, 4H), 2.95 (m, 4H), 2.38 (m, 2H), 1.60 (m, 2H), 1.64 (m,2H), 1.22 (s, 30H), 0.78 (t, 3H).

MQTS 1137—6.8 mg (19% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₅H₅₂N₄O₂: m/z 441; obsd 441 at 13.3 min. ¹H NMR (D₂O, δ): 3.96 (m,2H), 3.28 (m, 4H), 3.04 (m, 4H), 1.48 (m, 2H), 1.70 (m, 2H), 1.22 (s,30H), 0.82 (t, 3H).

MQTS 1142—3.2 mg (9% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₆H₅₄N₄O₂: m/z 455; obsd 455 at 13.3 min. ¹H NMR (D₂O, δ): 3.88 (m,2H), 3.26 (m, 4H), 2.96 (m, 4H), 2.78 (m, 2H), 1.83 (m, 2H), 1.65 (m,2H), 1.20 (s, 30H), 0.78 (t, 3H).

MQTS 1147—5.9 mg (16% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₇H₅₆N₄O₂: m/z 470; obsd 470 at 13.4 min. ¹H NMR (D₂O, δ): 3.81 (s,2H), 3.24 (t, 2H), 3.02 (m, 2H), 2.94 (t, 4H), 2.42 (t, 2H), 1.96 (m,2H), 1.82 (t, 2H), 1.66 (m, 2H), 1.15 (s, 30H), 0.76 (t, 3H).

MQTS 1227—6.1 mg (16% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₇H₅₆N₄O₂: m/z 469; obsd 469 at 13.3 min. ¹H NMR (D₂O, δ): 3.88 (s,2H), 3.12 (m, 2H), 2.92 (m, 4H), 1.63 (m, 4H), 1.43 (m, 2H), 1.18 (s,32H), 0.78 (t, 3H).

MQTS 1232—3.4 mg (9% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₈H₅₈N₄O₂: m/z 483; obsd 483 at 13.3 min. ¹H NMR (D₂O, δ): 3.82 (s,2H), 3.26 (t, 2H), 3.14 (t, 2H), 2.94 (m, 4H), 2.88 (t, 2H), 1.67 (m,4H), 1.47 (m, 2H), 1.23 (s, 32H), 0.79 (t, 3H).

MQTS 1237—5.3 mg (13% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₉H₆₀N₄O₂: m/z 497; obsd 497 at 13.0 min. ¹H NMR (D₂O, δ): 3.83 (s,2H), 3.17 (m, 2H), 2.94 (m, 4H), 2.43 (m, 2H), 1.96 (m, 2H), 1.64 (m,4H), 1.51 (m, 2H), 1.34 (m, 4H), 1.24 (s, 30H), 0.80 (t, 3H).

MQTS 2326—8.5 mg (25% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₄H₅₁N₃O₂: m/z 414; obsd 414 at 13.5 min. ¹H NMR (D₂O, δ): 3.90 (s,2H), 3.69 (m, 2H), 3.61 (m, 2H), 3.40 (m, 2H), 3.16 (m, 2H), 3.0 (m,2H), 1.70 (m, 2H), 1.21 (s, 30H), 0.78 (t, 3H).

MQTS 2328—4.2 mg (12% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₅H₅₃N₃O₂: m/z 428; obsd 428 at 13.6 min. ¹H NMR (D₂O, δ): 3.71 (m,2H), 3.58 (m, 2H), 3.37 (m, 2H), 2.23 (m, 2H), 3.16 (m, 2H), 3.00 (m,2H), 2.72 (m, 2H), 1.64 (m, 2H), 1.22 (s, 30H), 0.82 (t, 3H).

MQTS 2330—4.9 mg (16% yield) white solid is obtained. LC/MS calcd [M+H]for C₂₆H₅₅₀N₃O₂: m/z 442; obsd 442 at 14.7 min. ¹H NMR (D₂O, δ): 3.70(m, 2H), 3.58 (m, 2H), 3.49 (m, 2H), 3.22 (m, 2H), 3.18 (m, 4H), 2.96(m, 2H), 2.73 (m, 2H), 1.68 (m, 2H), 1.23 (m, 30H), 0.81 (t, 3H).

Rapid-throughput Fluorescence Displacement Assay for quantifying bindingaffinities to LPS. The BODIPY-TR-cadaverine (BC;(5-(((4-(4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a-diaza-s-indacene-3-yl)phenoxy)acetyl)amino)pentylamine, hydrochloride; obtained from Molecularprobes, Inc., Eugene, OR) displacement assay to quantify the affinitiesof binding of compounds to LPS has been described in detail recently.⁸¹This assay is performed in a rapid-throughput format as follows: thefirst column (16 wells) of a Corning Nonbinding Surface 384-wellflat-bottom black fluorescence microplate contain 15 test compounds pluspolymyxin B, all at 5 mM in DMSO, and are serially diluted two-fold in50 mM Tris buffer, pH 7.4, across the remaining 23 columns, achieving afinal dilution of 0.596 nM in a volume of 40 μ. Polymyxin B (PMB), apeptide antibiotic known to bind and neutralize LPS⁹⁵ serve as thepositive control and reference compound for every plate, enabling thequantitative assessment of repeatability and reproducibility (CV and Z′factors) for the assay. Automated liquid handling is performed on aPrecision 2000 automated microplate pipetting system, programmed usingthe Precision Power software, Bio-Tek Instruments Inc., VT, USA.

Nitric Oxide Assay. Nitric oxide production is measured as total nitritein murine macrophage J774A.1 cells using the Griess assay96 as describedpreviously.⁹⁴ J774A.1 cells are plated at ˜10⁵/ml in a volume of 40μl/well, in 384-well, flat-bottomed, cell culture treated microtiterplates and subsequently stimulated with 10 ng/ml lipopolysaccharide(LPS). Concurrent to LPS stimulation, serially diluted concentrations oftest compounds are added to the cell medium and left to incubateovernight for 16 h. Polymyxin B is used as reference compound in eachplate. Positive-(LPS stimulation only) and negative-controls (J774A. 1medium only) are included in each experiment. Nitrite concentrations aremeasured by adding 40 μl of supernatant to equal volumes of Griessreagents (50 μl/well; 0.1% NED solution in ddH₂O and 1% sulfanilamide,5% phosphoric acid solution in ddH₂O) and incubating for 15 minutes atroom temperature in the dark. Absorbance at 535 run is measured using aMolecular Devices Spectramax M2 multifunction plate reader (Sunnyvale,Calif.). Nitrite concentrations are interpolated from standard curvesobtained from serially diluted sodium nitrite standards. TABLE 1 Bindingaffinity (BC displacement; ED₅₀) and biological activity (NO inhibitionin murine J774 cells; IC₅₀) of leads following re-synthesis.

MQTS X m = R = n = ED₅₀ value (μM) IC₅₀ value (μM) 1002 —CH₂OCH₂— 1—CH₂Ph 0 12.4 17.6 1007 —CH₂OCH₂— 1 —CH₂Ph 1 2.54 2.79 1012 —CH₂OCH₂— 1—CH₂Ph 2 7.68 3.78 1032 —CH₂OCH₂— 1 —CH₂-imid 0 13.1 1.64 1037 —CH₂OCH₂—1 —CH₂-imid 1 3.17 1.88 1042 —CH₂OCH₂— 1 —CH₂-imid 2 5.38 1.86 1047—CH₂OCH₂— 1 —H 0 14.0 11.5 1052 —CH₂OCH₂— 1 —H 1 14.2 1.84 1057—CH₂OCH₂— 1 —H 2 10.8 3.33 1092 —CH₂— 1 —CH₂Ph 0 8.80 6.74 1097 —CH₂— 1—CH₂Ph 1 4.13 8.70 1102 —CH₂— 1 —CH₂Ph 2 5.75 3.42 1122 —CH₂— 1—CH₂-imid 0 4.87 6.90 1127 —CH₂— 1 —CH₂-imid 1 6.86 8.06 1132 —CH₂— 1—CH₂-imid 2 3.01 1.83 1137 —CH₂— 1 —H 0 6.61 7.94 1142 —CH₂— 1 —H 1 24205.26 1147 —CH₂— 1 —H 2 6.14 6.57 1187 —CH₂CH₂CH₂— 1 —CH₂Ph 1 3850 4.881192 —CH₂CH₂CH₂— 1 —CH₂Ph 2 7.51 4.80 1212 —CH₂CH₂CH₂— 1 —CH₂-imid 012.1 2.04 1222 —CH₂CH₂CH₂— 1 —CH₂-imid 2 18.7 0.90 1227 —CH₂CH₂CH₂— 1 —H0 28.2 3.27 1232 —CH₂CH₂CH₂— 1 —H 1 11.2 4.61 1237 —CH₂CH₂CH₂— 1 —H 29.77 3.22 2322 —CH₂— 0 — 0 3.80 5.56 2323 —CH₂— 0 — 1 9.92 7.49 2324—CH₂— 0 — 2 6.21 4.87 2325 —CH₂CH₂CH₂— 0 — 0 8.74 3.96 2326 —CH₂OCH₂— 0— 0 12.15 9.73 2327 —CH₂CH₂CH₂— 0 — 1 4.03 1.08 2328 —CH₂OCH₂— 0 — 19.16 6.54 2329 —CH₂CH₂CH₂— 0 — 2 7.61 2.07 2330 —CH₂OCH₂— 0 — 2 5.735.00

CHART 1 Solid-phase Lantern ™-based scaffold and combinatorial elements.

PORTION 1 PORTION 2 PORTION 3.x (N = 6) (N = 6) (N = 3)

PORTION 3.y (N = 5)

The pharmaceutically acceptable carriers described herein, for example,vehicles, adjuvants, excipients, or diluents, are well-known to thosewho are skilled in the art. Typically, the pharmaceutically acceptablecarrier is chemically inert to the active compounds and has nodetrimental side effects or toxicity under the conditions of use. Thepharmaceutically acceptable carriers can include polymers and polymermatrices.

The compounds of this disclosure can be administered by any conventionalmethod available for use in conjunction with pharmaceuticals, either asindividual therapeutic agents or in a combination of therapeutic agents.

The dosage administered will, of course, vary depending upon knownfactors, such as the pharmacodynamic characteristics of the particularagent and its mode and route of administration; the age, health andweight of the recipient; the nature and extent of the symptoms; the kindof concurrent treatment; the frequency of treatment; and the effectdesired. A daily dosage of active ingredient can be expected to be about0.001 to 1000 milligrams (mg) per kilogram (kg) of body weight, with thepreferred dose being 0.1 to about 30 mg/kg.

Dosage forms (compositions suitable for administration) contain fromabout 1 mg to about 500 mg of active ingredient per unit. In thesepharmaceutical compositions, the active ingredient will ordinarily bepresent in an amount of about 0.5-95% weight based on the total weightof the composition.

The active ingredient can be administered orally in solid dosage forms,such as capsules, tablets, and powders, or in liquid dosage forms, suchas elixirs, syrups and suspensions. It can also be administeredparenterally, in sterile liquid dosage forms. The active ingredient canalso be administered intranasally (nose drops) or by inhalation of adrug powder mist. Other dosage forms are potentially possible such asadministration transdermally, via patch mechanism or ointment. Theactive ingredient can be administered employing a sustained or delayedrelease delivery system or an immediate release delivery system.

Formulations suitable for oral administration can consist of (a) liquidsolutions, such as an effective amount of the compound dissolved indiluents, such as water, saline, or orange juice; (b) capsules, sachets,tablets, lozenges, and troches, each containing a predetermined amountof the active ingredient, as solids or granules; (c) powders; (d)suspensions in an appropriate liquid; and (e) suitable emulsions. Liquidformulations may include diluents, such as water and alcohols, forexample, ethanol, benzyl alcohol, propylene glycol, glycerin, and thepolyethylene alcohols, either with or without the addition of apharmaceutically acceptable surfactant, suspending agent, or emulsifyingagent. Capsule forms can be of the ordinary hard- or soft-shelledgelatin type containing, for example, surfactants, lubricants, and inertfillers, such as lactose, sucrose, calcium phosphate, and corn starch.Tablet forms can include one or more of the following: lactose, sucrose,mannitol, corn starch, potato starch, alginic acid, microcrystallinecellulose, acacia, gelatin, guar gum, colloidal silicon dioxide,croscarmellose sodium, talc, magnesium stearate, calcium stearate, zincstearate, stearic acid, and other excipients, colorants, diluents,buffering agents, disintegrating agents, moistening agents,preservatives, flavoring agents, and pharmacologically compatiblecarriers. Lozenge forms can comprise the active ingredient in a flavor,usually sucrose and acacia or tragacanth, as well as pastillescomprising the active ingredient in an inert base, such as gelatin andglycerin, or sucrose and acadia, emulsions, and gels containing, inaddition to the active ingredient, such carriers as are known in theart.

The compounds of the present disclosure, alone or in combination withother suitable components, can be made into aerosol formulations to beadministered via inhalation. These aerosol formulations can be placedinto pressurized acceptable propellants, such asdichlorodifluoromethane, propane, and nitrogen. They also may beformulated as pharmaceuticals for non-pressured preparations, such as ina nebulizer or an atomizer.

Formulations suitable for parenteral administration include aqueous andnon-aqueous, isotonic sterile injection solutions, which can containanti-oxidants, buffers, bacteriostats, and solutes that render theformulation isotonic with the blood of the intended recipient, andaqueous and non-aqueous sterile suspensions that can include suspendingagents, solubilizers, thickening agents, stabilizers, and preservatives.The compound can be administered in a physiologically acceptable diluentin a pharmaceutical carrier, such as a sterile liquid or mixture ofliquids, including water, saline, aqueous dextrose and related sugarsolutions, an alcohol, such as ethanol, isopropanol, or hexadecylalcohol, glycols, such as propylene glycol or polyethylene glycol suchas poly(ethyleneglycol) 400, glycerol ketals, such as2,2-dimethyl-1,3-dioxolane-4-methanol, ethers, an oil, a fatty acid, afatty acid ester or glyceride, or an acetylated fatty acid glyceridewith or without the addition of a pharmaceutically acceptablesurfactant, such as a soap or a detergent, suspending agent, such aspectin, carbomers, methylcellulose, hydroxypropylmethylcellulose, orcarboxymethylcellulose, or emulsifying agents and other pharmaceuticaladjuvants.

Oils, which can be used in parenteral formulations include petroleum,animal, vegetable, or synthetic oils. Specific examples of oils includepeanut, soybean, sesame, cottonseed, corn, olive, petrolatum, andmineral. Suitable fatty acids for use in parenteral formulations includeoleic acid, stearic acid, and isostearic acid. Ethyl oleate andisopropyl myristate are examples of suitable fatty acid esters. Suitablesoaps for use in parenteral formulations include fatty alkali metal,ammonium, and triethanolamine salts, and suitable detergents include (a)cationic detergents such as, for example, dimethyldialkylammoniumhalides, and alkylpyridinium halides, (b) anionic detergents such as,for example, alkyl, aryl, and olefin sulfonates, alkyl, olefin, ether,and monoglyceride sulfates, and sulfosuccinates, (c) nonionic detergentssuch as, for example, fatty amine oxides, fatty acid alkanolamides, andpolyoxyethylene polypropylene copolymers, (d) amphoteric detergents suchas, for example, alkyl β-aminopropionates, and 2-alkylimidazolinequaternary ammonium salts, and (e) mixtures thereof.

The parenteral formulations typically contain from about 0.5% to about25% by weight of the active ingredient in solution. Suitablepreservatives and buffers can be used in such formulations. In order tominimize or eliminate irritation at the site of injection, suchcompositions may contain one or more nonionic surfactants having ahydrophile-lipophile balance (HLB) of from about 12 to about 17. Thequantity of surfactant in such formulations ranges from about 5% toabout 15% by weight. Suitable surfactants include polyethylene sorbitanfatty acid esters, such as sorbitan monooleate and the high molecularweight adducts of ethylene oxide with a hydrophobic base, formed by thecondensation of propylene oxide with propylene glycol.

Pharmaceutically acceptable excipients are also well-known to those whoare skilled in the art. The choice of excipient will be determined inpart by the particular compound, as well as by the particular methodused to administer the composition. Accordingly, there is a wide varietyof suitable formulations of the pharmaceutical composition of thepresent invention. The following methods and excipients are merelyexemplary and are in no way limiting. The pharmaceutically acceptableexcipients preferably do not interfere with the action of the activeingredients and do not cause adverse side-effects. Suitable carriers andexcipients include solvents such as water, alcohol, and propyleneglycol, solid absorbants and diluents, surface active agents, suspendingagent, tableting binders, lubricants, flavors, and coloring agents.

The formulations can be presented in unit-dose or multi-dose sealedcontainers, such as ampules and vials, and can be stored in afreeze-dried (lyophilized) condition requiring only the addition of thesterile liquid excipient, for example, water, for injections,immediately prior to use. Extemporaneous injection solutions andsuspensions can be prepared from sterile powders, granules, and tablets.The requirements for effective pharmaceutical carriers for injectablecompositions are well known to those of ordinary skill in the art. SeePharmaceutics and Pharmacy Practice, J. B. Lippincott Co., Philadelphia,Pa., Banker and Chalmers, Eds., 238-250 (1982) and ASHP Handbook onInjectable Drugs, Toissel, 4th ed., 622-630 (1986).

Formulations suitable for topical administration include lozengescomprising the active ingredient in a flavor, usually sucrose and acaciaor tragacanth; pastilles comprising the active ingredient in an inertbase, such as gelatin and glycerin, or sucrose and acacia; and mouthwashes comprising the active ingredient in a suitable liquid carrier; aswell as creams, emulsions, and gels containing, in addition to theactive ingredient, such carriers as are known in the art.

Additionally, formulations suitable for rectal administration may bepresented as suppositories by mixing with a variety of bases such asemulsifying bases or water-soluble bases. Formulations suitable forvaginal administration may be presented as pessaries, tampons, creams,gels, pastes, foams, or spray formulas containing, in addition to theactive ingredient, such carriers as are known in the art to beappropriate.

Suitable pharmaceutical carriers are described in Remington'sPharmaceutical Sciences, Mack Publishing Company, a standard referencetext in this field.

The dose administered to an animal, particularly a human, in the contextof the present invention should be sufficient to affect a therapeuticresponse in the animal over a reasonable time frame. One skilled in theart will recognize that dosage will depend upon a variety of factorsincluding a condition of the animal, the body weight of the animal, aswell as the condition being treated.

A suitable dose is that which will result in a concentration of theactive agent in a patient which is known to affect the desired response.

The size of the dose also will be determined by the route, timing andfrequency of administration as well as the existence, nature, and extentof any adverse side effects that might accompany the administration ofthe compound and the desired physiological effect.

Usefull pharmaceutical dosage forms for administration of the compoundsaccording to the present invention can be illustrated as follows:

Hard Shell Capsules

A large number of unit capsules are prepared by filling standardtwo-piece hard gelatine capsules each with 100 mg of powdered activeingredient, 150 mg of lactose, 50 mg of cellulose and 6 mg of magnesiumstearate.

Soft Gelatin Capsules

A mixture of active ingredient in a digestible oil such as soybean oil,cottonseed oil or olive oil is prepared and injected by means of apositive displacement pump into molten gelatin to form soft gelatincapsules containing 100 mg of the active ingredient. The capsules arewashed and dried. The active ingredient can be dissolved in a mixture ofpolyethylene glycol, glycerin and sorbitol to prepare a water misciblemedicine mix.

The foregoing description illustrates and describes the presentdisclosure. Additionally, the disclosure shows and describes only thepreferred embodiments of the disclosure, but, as mentioned above, it isto be understood that it is capable of changes or modifications withinthe scope of the concept as expressed herein, commensurate with theabove teachings and/or the skill or knowledge of the relevant art. Theembodiments described hereinabove are further intended to explain bestmodes known of practicing the invention and to enable others skilled inthe art to utilize the disclosure in such, or other, embodiments andwith the various modifications required by the particular applicationsor uses disclosed herein. Accordingly, the description is not intendedto limit the invention to the form disclosed herein. Also, it isintended that the appended claims be construed to include alternativeembodiments.

The term “comprising” (and its grammatical variations) as used herein isused in the inclusive sense of “having” or “including” and not in theexclusive sense of “consisting only of”.

All publications, patents and patent applications cited in thisspecification are herein incorporated by reference, and for any and allpurposes, as if each individual publication, patent or patentapplication were specifically and individually indicates to beincorporated by reference. In the case of inconsistencies, the presentdisclosure will prevail.

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1-2. (canceled)
 3. A compound

pharmaceutically acceptable salts thereof; and prodrugs-thereof.
 4. Thecompound of claim 3 being represented by the formula:


5. The compound of claim 3 being represented by the formula:


6. The compound of claim 3 being represented by the formula:


7. The compound of claim 3 being represented by the formula:


8. A pharmaceutical composition comprising a compound according to claim3.
 9. A pharmaceutical composition comprising a compound according toclaim
 4. 10. A pharmaceutical composition comprising a compoundaccording to claim
 5. 11. A pharmaceutical composition comprising acompound according to claim
 6. 12. A pharmaceutical compositioncomprising a compound according to claim
 7. 13-32. (canceled)